GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Dinoroseobacter shibae DFL-12

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate 3607836 Dshi_1244 Dihydroxy-acid dehydratase (RefSeq)

Query= curated2:P31961
         (608 letters)



>FitnessBrowser__Dino:3607836
          Length = 569

 Score =  172 bits (436), Expect = 3e-47
 Identities = 148/511 (28%), Positives = 236/511 (46%), Gaps = 43/511 (8%)

Query: 68  VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127
           + I + ++++   +         +K+ + E G    F    P M  G TQ +P    ++ 
Sbjct: 41  IGICNTWSELTPCNHGLRTLAEGVKRGVWEAGG---FPVEFPVMSLGETQMKP---TAML 94

Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGI-- 185
            R+++AM    ++     D  + LG CDK  PG L+G+     LP++ V AGPM  G   
Sbjct: 95  FRNLLAMDVEESIRAYGMDGVVLLGGCDKTTPGQLMGAASVD-LPSIVVSAGPMLNGKYR 153

Query: 186 -----SNKEKAAVRQLFAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLH 240
                S  +     +    G+ T  + + +E     + G C   GTA+T   LVE MG+ 
Sbjct: 154 GQDIGSGTDVWKFSEAVRAGEMTLADFMNAEAGMSRSAGVCMTMGTASTMASLVEAMGMS 213

Query: 241 LPGASFVNPNTPLRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGS 300
           LP  + +      R  L     ++   +  E+   +  + I+ + A  N+++A  A GGS
Sbjct: 214 LPLNAALPAVDARRMALAHLTGKRIVEMVEED---LRPSAILTKPAFENAILANAAVGGS 270

Query: 301 TNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQL 360
           TN  +HLLA+A  AG+ LT +D  E+   +P L    P+G+  +  F  AGGM  ++ +L
Sbjct: 271 TNAVMHLLALAGRAGVDLTLKDF-EIGGEIPLLVNCMPSGKYLMEDFAYAGGMPVVLSEL 329

Query: 361 LDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGL 420
            D         TV G  +  YT             EG E   +  ++   D P     GL
Sbjct: 330 RDH---LRPATTVLGKDIAAYT-------------EGAE-CFNRDVIHAYDAPVKPAAGL 372

Query: 421 RLMEGNLGR--GVMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELE--RDLVAVVRF 476
           R++ G+L     ++K SA        E P  +F +   + A     +L    D + V++ 
Sbjct: 373 RVLRGSLAPDGAIVKPSAATDALLEHEGPAFVFENIEDMKANIDRDDLPITPDTILVLKG 432

Query: 477 QGPRAN-GMPELHKLTPFLGVLQDRGFKVALVTDGRMSG-ASGKVPAAIHVSPEAIAGGP 534
            GP+   GMPE+  +     ++++    +  V+D RMSG A G V   +HV+PEA AGGP
Sbjct: 433 CGPKGYPGMPEVGNMPIPAKLVREGVRDMIRVSDARMSGTAYGTV--ILHVAPEAQAGGP 490

Query: 535 LARLRDGDRVRVDGVNGELRVLVDDAEWQAR 565
           LA ++ GDR+RV    G L +LVD  E  AR
Sbjct: 491 LALVKTGDRIRVSAREGVLDLLVDATELAAR 521


Lambda     K      H
   0.319    0.135    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 790
Number of extensions: 56
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 608
Length of database: 569
Length adjustment: 37
Effective length of query: 571
Effective length of database: 532
Effective search space:   303772
Effective search space used:   303772
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory